Understanding protein-DNA interaction is essential in the fight of diseases at the genetic level. Restriction endonucleases are excellent model systems to study protein-DNA interaction because of their high specificity towards their recognition sequence. They are part of restriction-modification systems and serve as a primitive immune system in bacterial cells against bacteriophage infection by cutting the phage DNA with high specificity, while the host DNA is protected by a specific methylation within the recognition sequence. Additionally, the high specificity gives restriction endonucleases an important role in recombinant DNA technologies. I propose to study the structure-function of the FokI restriction endonuclease using a combination of biophysical methods. FokI belongs to a special subgroup of bipartite enzymes that cleave DNA nonspecifically at a defined distance outside of a non- palindromic recognition sequence. The bipartite nature of FoAl makes it an excellent candidate for the design of artificial enzymes. The studies will provide further understanding how recognition and catalysis are coupled (or de-coupled) in restriction endonucleases and will aid the design of restriction enzymes with new specificities.